diff --git a/tests_integration/nativeapp/test_deploy.py b/tests_integration/nativeapp/test_deploy.py
index 52ab389b8..e85d57457 100644
--- a/tests_integration/nativeapp/test_deploy.py
+++ b/tests_integration/nativeapp/test_deploy.py
@@ -500,7 +500,7 @@ def test_nativeapp_deploy_looks_for_prefix_matches(
             )
             project_definition_file["native_app"]["artifacts"].append("src")
             project_definition_file["native_app"]["artifacts"].append(
-                "lib/parent/child"
+                {"src": "lib/parent", "dest": "parent-lib"}
             )
             snowflake_yml.write_text(yaml.dump(project_definition_file))
 
@@ -510,7 +510,7 @@ def test_nativeapp_deploy_looks_for_prefix_matches(
             touch(str(project_dir / "lib/parent/child/b.py"))
             touch(str(project_dir / "lib/parent/child/c/c.py"))
 
-            result = runner.invoke_with_connection_json(
+            result = runner.invoke_with_connection(
                 ["app", "deploy", "-r", "app"],
                 env=TEST_ENV,
             )
@@ -527,55 +527,72 @@ def test_nativeapp_deploy_looks_for_prefix_matches(
                 stage_files.json, {"name": "stage/setup_script.sql"}
             )
             assert contains_row_with(stage_files.json, {"name": "stage/README.md"})
-            assert not_contains_row_with(stage_files.json, {"name": "src/main.py"})
+            assert not_contains_row_with(
+                stage_files.json, {"name": "stage/src/main.py"}
+            )
+            assert not_contains_row_with(
+                stage_files.json, {"name": "stage/parent-lib/child/c/c.py"}
+            )
 
-            result = runner.invoke_with_connection_json(
+            result = runner.invoke_with_connection(
                 ["app", "deploy", "-r", "lib/parent/child/c"],
                 env=TEST_ENV,
             )
             assert result.exit_code == 0
+            stage_files = runner.invoke_with_connection_json(
+                ["stage", "list-files", f"{package_name}.{stage_name}"],
+                env=TEST_ENV,
+            )
             assert contains_row_with(
-                stage_files.json, {"name": "lib/parent/child/c/c.py"}
+                stage_files.json, {"name": "stage/parent-lib/child/c/c.py"}
             )
             assert not_contains_row_with(
-                stage_files.json, {"name": "lib/parent/child/a.py"}
+                stage_files.json, {"name": "stage/parent-lib/child/a.py"}
             )
             assert not_contains_row_with(
-                stage_files.json, {"name": "lib/parent/child/b.py"}
+                stage_files.json, {"name": "stage/parent-lib/child/b.py"}
             )
 
-            result = runner.invoke_with_connection_json(
+            result = runner.invoke_with_connection(
                 ["app", "deploy", "lib/parent/child/a.py"],
                 env=TEST_ENV,
             )
             assert result.exit_code == 0
+            stage_files = runner.invoke_with_connection_json(
+                ["stage", "list-files", f"{package_name}.{stage_name}"],
+                env=TEST_ENV,
+            )
             assert contains_row_with(
-                stage_files.json, {"name": "lib/parent/child/c/c.py"}
+                stage_files.json, {"name": "stage/parent-lib/child/c/c.py"}
             )
             assert contains_row_with(
-                stage_files.json, {"name": "lib/parent/child/a.py"}
+                stage_files.json, {"name": "stage/parent-lib/child/a.py"}
             )
             assert not_contains_row_with(
-                stage_files.json, {"name": "lib/parent/child/b.py"}
+                stage_files.json, {"name": "stage/parent-lib/child/b.py"}
             )
 
-            result = runner.invoke_with_connection_json(
+            result = runner.invoke_with_connection(
                 ["app", "deploy", "lib", "-r"],
                 env=TEST_ENV,
             )
             assert result.exit_code == 0
+            stage_files = runner.invoke_with_connection_json(
+                ["stage", "list-files", f"{package_name}.{stage_name}"],
+                env=TEST_ENV,
+            )
             assert contains_row_with(
-                stage_files.json, {"name": "lib/parent/child/c/c.py"}
+                stage_files.json, {"name": "stage/parent-lib/child/c/c.py"}
             )
             assert contains_row_with(
-                stage_files.json, {"name": "lib/parent/child/a.py"}
+                stage_files.json, {"name": "stage/parent-lib/child/a.py"}
             )
             assert contains_row_with(
-                stage_files.json, {"name": "lib/parent/child/b.py"}
+                stage_files.json, {"name": "stage/parent-lib/child/b.py"}
             )
 
         finally:
-            result = runner.invoke_with_connection_json(
+            result = runner.invoke_with_connection(
                 ["app", "teardown", "--force"],
                 env=TEST_ENV,
             )